project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_suseth:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_suseth
    outputs:
      highly_sensitive:
        cohort: output/input_suseth.csv

  generate_study_pop_covdischarged:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covdischarged
    outputs:
      highly_sensitive:
        cohort: output/input_covdischarged.csv

  generate_study_pop_pneum2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneum2019
    outputs:
      highly_sensitive:
        cohort: output/input_pneum2019.csv

  generate_study_pop_flu2017_19:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flu2017_19
    outputs:
      highly_sensitive:
        cohort: output/input_flu2017_19.csv

        
  generate_2019pool02:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool02
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool02.csv        

  generate_2019pool02_ALT:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019 --index-date-range "2019-02-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2019_2019-02-01.csv        

  generate_2019pool03:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool03
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool03.csv        

  generate_2019pool04:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool04
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool04.csv        

  generate_2019pool05:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool05
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool05.csv        

  generate_2019pool06:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool06
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool06.csv        

  generate_2019pool07:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool07
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool07.csv        

  generate_2019pool08:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool08
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool08.csv        
           
  generate_2019pool09:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool09
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool09.csv        

  generate_2019pool10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool10
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool10.csv        
      
  generate_2019pool11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool11
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool11.csv        

  generate_2019pool12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool12
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool12.csv        
                   
  create_covid:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do COVID
    needs: [generate_study_pop_covdischarged]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_COVID.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_COVID.log

  create_pneum2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do PNEUM 
    needs: [generate_study_pop_pneum2019]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_PNEUM.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_PNEUM.log
 
  create_flu2017_19:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do FLU 
    needs: [generate_study_pop_flu2017_19]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_FLU.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_FLU.log

  create_2019pool02:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 02
    needs: [generate_2019pool02]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_02.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_02.log

  create_2019pool03:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 03
    needs: [generate_2019pool03]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_03.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_03.log

  create_2019pool04:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 04
    needs: [generate_2019pool04]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_04.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_04.log

  create_2019pool05:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 05
    needs: [generate_2019pool05]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_05.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_05.log

  create_2019pool06:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 06
    needs: [generate_2019pool06]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_06.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_06.log

  create_2019pool07:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 07
    needs: [generate_2019pool07]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_07.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_07.log

  create_2019pool08:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 08
    needs: [generate_2019pool08]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_08.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_08.log

  create_2019pool09:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 09
    needs: [generate_2019pool09]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_09.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_09.log

  create_2019pool10:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 10
    needs: [generate_2019pool10]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_10.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_10.log

  create_2019pool11:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 11
    needs: [generate_2019pool11]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_11.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_11.log

  create_2019pool12:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 12
    needs: [generate_2019pool12]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_12.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_12.log


  getmatches2019:
    run: stata-mp:latest analysis/cr_getmatches2019.do
    needs:
      - create_covid
      - create_2019pool02
      - create_2019pool03
      - create_2019pool04
      - create_2019pool05
      - create_2019pool06
      - create_2019pool07
      - create_2019pool08
      - create_2019pool09
      - create_2019pool10
      - create_2019pool11
      - create_2019pool12
    outputs:
      highly_sensitive:
        cohort: analysis/cr_getmatches2019.dta
      moderately_sensitive:
        log: analysis/output/cr_getmatches2019.log

  appenddata:
    run: stata-mp:latest analysis/cr_append_process_data.do
    needs:
      - create_covid
      - create_pneum2019
      - create_flu2017_19
      - generate_suseth
      - getmatches2019
    outputs:
      highly_sensitive:
        cohort: analysis/cr_append_process_data.dta
      moderately_sensitive:
        log: analysis/output/cr_append_process_data.log

  andescriptives_models:
    run: stata-mp:latest analysis/model_descriptives_models.do
    needs: 
      - generate_study_pop_covdischarged
      - appenddata
    outputs:
      moderately_sensitive:
        logs: analysis/output/*.log 
        tables: analysis/output/an_*.txt
        figures: analysis/output/an_cumulativeincidence*.svg
        timefig: analysis/output/an_desc*.svg
        models: analysis/output/models/an_cox*.ster

  ancoxMI:
    run: stata-mp:latest analysis/an_cox_R2.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_R2.log
        models: analysis/output/models/an_cox_R2*.ster
         
  anFGcirculatory:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do circulatory 23498
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2circulatory.log
        models: analysis/output/models/an_FG_causespecific_R2circulatory*.ster
 
  anFGcancer_ex_nmsc:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do cancer_ex_nmsc 54668
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_FG_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anFGrespiratory:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do respiratory 1309
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2respiratory.log
        models: analysis/output/models/an_FG_causespecific_R2respiratory*.ster
 
 
  anFGrespiratorylrti:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do respiratorylrti 235
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_FG_causespecific_R2respiratorylrti*.ster
  
  
  anFGdigestive:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do digestive 32463
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2digestive.log
        models: analysis/output/models/an_FG_causespecific_R2digestive*.ster
  
  
  anFGmentalhealth:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do mentalhealth 25465
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_FG_causespecific_R2mentalhealth*.ster
  
 
  anFGnervoussystem:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do nervoussystem 2355
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_FG_causespecific_R2nervoussystem*.ster
  
  
  anFGgenitourinary:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do genitourinary 239802
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2genitourinary.log
        models: analysis/output/models/an_FG_causespecific_R2genitourinary*.ster
  
  
  anFGendo_nutr_metabol:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do endo_nutr_metabol 155545
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_FG_causespecific_R2endo_nutr_metabol*.ster
  
  
  anFGexternal:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do external 125554
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2external.log
        models: analysis/output/models/an_FG_causespecific_R2external*.ster
  
  
  anFGmusculoskeletal:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do musculoskeletal 124
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_FG_causespecific_R2musculoskeletal*.ster
  
  
  anFGotherinfections:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do otherinfections 789
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2otherinfections.log
        models: analysis/output/models/an_FG_causespecific_R2otherinfections*.ster

  anCOXr2circulatory:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do circulatory 23498
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2circulatory.log
        models: analysis/output/models/an_cox_causespecific_R2circulatory*.ster
 
  anCOXr2cancer_ex_nmsc:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do cancer_ex_nmsc 54668
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_cox_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anCOXr2respiratory:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do respiratory 1309
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2respiratory.log
        models: analysis/output/models/an_cox_causespecific_R2respiratory*.ster
 
 
  anCOXr2respiratorylrti:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do respiratorylrti 235
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_cox_causespecific_R2respiratorylrti*.ster
  
  
  anCOXr2digestive:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do digestive 32463
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2digestive.log
        models: analysis/output/models/an_cox_causespecific_R2digestive*.ster
  
  
  anCOXr2mentalhealth:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do mentalhealth 25465
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_cox_causespecific_R2mentalhealth*.ster
  
 
  anCOXr2nervoussystem:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do nervoussystem 2355
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_cox_causespecific_R2nervoussystem*.ster
  
  
  anCOXr2genitourinary:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do genitourinary 239802
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2genitourinary.log
        models: analysis/output/models/an_cox_causespecific_R2genitourinary*.ster
  
  
  anCOXr2endo_nutr_metabol:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do endo_nutr_metabol 155545
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_cox_causespecific_R2endo_nutr_metabol*.ster
  
  
  anCOXr2external:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do external 125554
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2external.log
        models: analysis/output/models/an_cox_causespecific_R2external*.ster
  
  
  anCOXr2musculoskeletal:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do musculoskeletal 124
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_cox_causespecific_R2musculoskeletal*.ster
  
  
  anCOXr2otherinfections:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do otherinfections 789
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2otherinfections.log
        models: analysis/output/models/an_cox_causespecific_R2otherinfections*.ster


  ancoxbytime:
    run: stata-mp:latest analysis/an_coxbytime_R2.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_R2.log
        models: analysis/output/models/an_coxbytime_R2*.ster

  anFGbytimecirculatory:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do circulatory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2circulatory.log
        models: analysis/output/models/an_FGbytime_causespecific_R2circulatory*.ster
 
  anFGbytimecancer_ex_nmsc:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do cancer_ex_nmsc 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_FGbytime_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anFGbytimerespiratory:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do respiratory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2respiratory.log
        models: analysis/output/models/an_FGbytime_causespecific_R2respiratory*.ster
 
 
  anFGbytimerespiratorylrti:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do respiratorylrti 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_FGbytime_causespecific_R2respiratorylrti*.ster
  
  
  anFGbytimedigestive:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do digestive 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2digestive.log
        models: analysis/output/models/an_FGbytime_causespecific_R2digestive*.ster
  
  
  anFGbytimementalhealth:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do mentalhealth 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_FGbytime_causespecific_R2mentalhealth*.ster
  
 
  anFGbytimenervoussystem:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do nervoussystem 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_FGbytime_causespecific_R2nervoussystem*.ster
  
  
  anFGbytimegenitourinary:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do genitourinary 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2genitourinary.log
        models: analysis/output/models/an_FGbytime_causespecific_R2genitourinary*.ster
  
  
  anFGbytimeendo_nutr_metabol:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do endo_nutr_metabol 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_FGbytime_causespecific_R2endo_nutr_metabol*.ster
  
  
  anFGbytimeexternal:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do external 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2external.log
        models: analysis/output/models/an_FGbytime_causespecific_R2external*.ster
  
  
  anFGbytimemusculoskeletal:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do musculoskeletal 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_FGbytime_causespecific_R2musculoskeletal*.ster
  
  
  anFGbytimeotherinfections:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do otherinfections 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2otherinfections.log
        models: analysis/output/models/an_FGbytime_causespecific_R2otherinfections*.ster


  anCOXr2bytimecirculatory:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do circulatory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2circulatory.log
        models: analysis/output/models/an_coxbytime_causespecific_R2circulatory*.ster
 
  anCOXr2bytimecancer_ex_nmsc:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do cancer_ex_nmsc 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_coxbytime_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anCOXr2bytimerespiratory:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do respiratory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2respiratory.log
        models: analysis/output/models/an_coxbytime_causespecific_R2respiratory*.ster
 
 
  anCOXr2bytimerespiratorylrti:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do respiratorylrti 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_coxbytime_causespecific_R2respiratorylrti*.ster
  
  
  anCOXr2bytimedigestive:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do digestive 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2digestive.log
        models: analysis/output/models/an_coxbytime_causespecific_R2digestive*.ster
  
  
  anCOXr2bytimementalhealth:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do mentalhealth 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_coxbytime_causespecific_R2mentalhealth*.ster
  
 
  anCOXr2bytimenervoussystem:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do nervoussystem 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_coxbytime_causespecific_R2nervoussystem*.ster
  
  
  anCOXr2bytimegenitourinary:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do genitourinary 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2genitourinary.log
        models: analysis/output/models/an_coxbytime_causespecific_R2genitourinary*.ster
  
  
  anCOXr2bytimeendo_nutr_metabol:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do endo_nutr_metabol 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_coxbytime_causespecific_R2endo_nutr_metabol*.ster
  
  
  anCOXr2bytimeexternal:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do external 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2external.log
        models: analysis/output/models/an_coxbytime_causespecific_R2external*.ster
  
  
  anCOXr2bytimemusculoskeletal:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do musculoskeletal 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_coxbytime_causespecific_R2musculoskeletal*.ster
  
  
  anCOXr2bytimeotherinfections:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do otherinfections 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2otherinfections.log
        models: analysis/output/models/an_coxbytime_causespecific_R2otherinfections*.ster
  
 
  anprocess_forestplots:
    run: stata-mp:latest analysis/model_forestplots.do
    needs: [andescriptives_models]
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_*.svg 

  anprocess_forestplots_CoxR2:
    run: stata-mp:latest analysis/an_processout_regressionmodels_FOREST_R2.do
    needs: [ancoxMI]
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_regressionmodels_FOREST_R2_COX.svg 

  anprocess_forestplots_CoxCauseSpecificR2:
    run: stata-mp:latest analysis/an_processout_coxcausespecific_R2_FOREST.do
    needs: 
      - anCOXr2circulatory
      - anCOXr2cancer_ex_nmsc 
      - anCOXr2respiratory
      - anCOXr2respiratorylrti
      - anCOXr2digestive
      - anCOXr2mentalhealth
      - anCOXr2nervoussystem
      - anCOXr2genitourinary
      - anCOXr2endo_nutr_metabol
      - anCOXr2external
      - anCOXr2musculoskeletal
      - anCOXr2otherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_coxcausespecific_R2_FOREST.svg 


  anprocess_forestplots_FG:
    run: stata-mp:latest analysis/an_processout_FGcausespecific_FOREST_R2.do
    needs: 
      - anFGcirculatory
      - anFGcancer_ex_nmsc 
      - anFGrespiratory
      - anFGrespiratorylrti
      - anFGdigestive
      - anFGmentalhealth
      - anFGnervoussystem
      - anFGgenitourinary
      - anFGendo_nutr_metabol
      - anFGexternal
      - anFGmusculoskeletal
      - anFGotherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_FGcausespecific_R2_FOREST.svg 

  anprocess_forestplots_coxbytime:
    run: stata-mp:latest analysis/an_processout_coxbytime_FOREST.do
    needs: 
      - ancoxbytime
      - anCOXr2bytimecirculatory
      - anCOXr2bytimecancer_ex_nmsc 
      - anCOXr2bytimerespiratory
      - anCOXr2bytimerespiratorylrti
      - anCOXr2bytimedigestive
      - anCOXr2bytimementalhealth
      - anCOXr2bytimenervoussystem
      - anCOXr2bytimegenitourinary
      - anCOXr2bytimeendo_nutr_metabol
      - anCOXr2bytimeexternal
      - anCOXr2bytimemusculoskeletal
      - anCOXr2bytimeotherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_coxbytime_FOREST.svg 

  anphchecks:
    run: stata-mp:latest analysis/an_phchecks.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_phchecks.log

  ansensanal:
    run: stata-mp:latest analysis/an_sensanalyses.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_sensanalyses.log
        models: analysis/output/models/an_sensanalyses*.ster

  an_SAcirculatory:
    run: stata-mp:latest analysis/an_SAcausespecific.do circulatory 345
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificcirculatory.log
        models: analysis/output/models/an_SAcausespecificcirculatory*.ster

  an_SAcancer_ex_nmsc:
    run: stata-mp:latest analysis/an_SAcausespecific.do cancer_ex_nmsc 6266
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificcancer_ex_nmsc.log
        models: analysis/output/models/an_SAcausespecificcancer_ex_nmsc*.ster

  an_SArespiratory:
    run: stata-mp:latest analysis/an_SAcausespecific.do respiratory 7883
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificrespiratory.log
        models: analysis/output/models/an_SAcausespecificrespiratory*.ster

  an_SArespiratorylrti:
    run: stata-mp:latest analysis/an_SAcausespecific.do respiratorylrti 40905
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificrespiratorylrti.log
        models: analysis/output/models/an_SAcausespecificrespiratorylrti*.ster

  an_SAdigestive:
    run: stata-mp:latest analysis/an_SAcausespecific.do digestive 3985
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificdigestive.log
        models: analysis/output/models/an_SAcausespecificdigestive*.ster

  an_SAmentalhealth:
    run: stata-mp:latest analysis/an_SAcausespecific.do mentalhealth 347
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificmentalhealth.log
        models: analysis/output/models/an_SAcausespecificmentalhealth*.ster

  an_SAnervoussystem:
    run: stata-mp:latest analysis/an_SAcausespecific.do nervoussystem 23
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificnervoussystem.log
        models: analysis/output/models/an_SAcausespecificnervoussystem*.ster

  an_SAgenitourinary:
    run: stata-mp:latest analysis/an_SAcausespecific.do genitourinary 4556
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificgenitourinary.log
        models: analysis/output/models/an_SAcausespecificgenitourinary*.ster

  an_SAendo_nutr_metabol:
    run: stata-mp:latest analysis/an_SAcausespecific.do endo_nutr_metabol 5995
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificendo_nutr_metabol.log
        models: analysis/output/models/an_SAcausespecificendo_nutr_metabol*.ster

  an_SAexternal:
    run: stata-mp:latest analysis/an_SAcausespecific.do external 2068
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificexternal.log
        models: analysis/output/models/an_SAcausespecificexternal*.ster

  an_SAmusculoskeletal:
    run: stata-mp:latest analysis/an_SAcausespecific.do musculoskeletal 92885
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificmusculoskeletal.log
        models: analysis/output/models/an_SAcausespecificmusculoskeletal*.ster

  an_SAotherinfections:
    run: stata-mp:latest analysis/an_SAcausespecific.do otherinfections 158
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificotherinfections.log
        models: analysis/output/models/an_SAcausespecificotherinfections*.ster

  anprocessoutSA:
    run: stata-mp:latest analysis/an_processout_SAresults.do
    needs: 
      - ancoxMI
      - anCOXr2circulatory
      - anCOXr2cancer_ex_nmsc
      - anCOXr2respiratory
      - anCOXr2respiratorylrti
      - anCOXr2digestive
      - anCOXr2mentalhealth
      - anCOXr2nervoussystem
      - anCOXr2genitourinary
      - anCOXr2endo_nutr_metabol
      - anCOXr2external
      - anCOXr2musculoskeletal
      - anCOXr2otherinfections  
      - anFGcirculatory
      - anFGcancer_ex_nmsc
      - anFGrespiratory
      - anFGrespiratorylrti
      - anFGdigestive
      - anFGmentalhealth
      - anFGnervoussystem
      - anFGgenitourinary
      - anFGendo_nutr_metabol
      - anFGexternal
      - anFGmusculoskeletal
      - anFGotherinfections  
      - an_SAcirculatory
      - an_SAcancer_ex_nmsc
      - an_SArespiratory
      - an_SArespiratorylrti
      - an_SAdigestive
      - an_SAmentalhealth
      - an_SAnervoussystem
      - an_SAgenitourinary
      - an_SAendo_nutr_metabol
      - an_SAexternal
      - an_SAmusculoskeletal
      - an_SAotherinfections
    outputs:
      moderately_sensitive:
        log: analysis/output/an_processout_SAresults.log

  runsingledofile:
    run: stata-mp:latest analysis/an_descriptive.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_descriptive.log
        table: analysis/output/an_descriptive_OUTCOMES.txt
        histogram: analysis/output/an_descriptive_EVENTSBYTIME.svg

  rundescriptivetablealone:
    run: stata-mp:latest analysis/an_desctable.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        tables: analysis/output/an_desctable*.txt

  runKMsalone:
    run: stata-mp:latest analysis/an_cumulativeincidence.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        kmcis: analysis/output/an_cumulativeinc*.svg
    

  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_study_pop_covdischarged]
    outputs:
      moderately_sensitive:
        log: logs/model.log